Overnight the Australian Navy made a mid-ocean transfer of more than 40 asylum seekers to Basarnas.

The 44 asylum seekers and two crew members were on a boat which issued a distress call 40 nautical miles off Java on Thursday morning.

Suyatno, the head of operations at the Jakarta office of Indonesia's rescue agency Basarnas, says his agency did not have the capability to reach the boat.

The Australian Navy intercepted the vessel and then advised Basarnas that it would drop the asylum seekers off.

In the early hours of Friday morning an Indonesian rescue crew met a Navy ship off the coast of Java and the asylum seekers were handed over.

It is understood the handover took place just outside the 12 nautical mile limit of Indonesian territorial waters.

Suyatno says he does not know why Australia did not take the asylum seekers to Christmas Island.

One of the boat's crew members, Azam, says the boat was not broken, despite passengers calling Australia to be rescued.

He says the Navy set fire to the boat at sea.

The passengers and crew have been returned to the Indonesian mainland.

Asylum seekers only handed back to Indonesia once before

An interception of this kind, where the Australian Navy hands asylum seekers back to Indonesian authorities after being asked to assist in their rescue, only happened once during the six years of the last Labor government.

On that occasion, last year, a boat sank near the mouth of the Sunda Strait off west Java.

Indonesia now says briefing note sent by mistake

A war of words broke out yesterday when the office of Indonesian foreign minister Marty Natalegawa sent out a detailed summary of a private meeting the minister held with his Australian counterpart Julie Bishop in New York earlier this week.

The email said the foreign ministers discussed the Coalition's plans to turn back asylum boats and noted that Australia wanted to work on the issue "behind the scenes" and "quietly".

It also warned Australia's plans to turn back asylum seeker boats could jeopardise trust and cooperation between the two countries.

That prompted former Liberal foreign minister Alexander Downer to use an appearance on ABC TV to issue a pointed rebuke to Dr Natalegawa, saying Indonesian crews are breaching Australian sovereignty and he should not be "taking shots" at the Coalition.

But today Indonesia's foreign ministry issued a "correction", saying the information in the briefing note was not intended for the media, that the meeting was private, and there was no official press release.

"Information [from that meeting] is now being quoted in several media outlets to create the impression of discord among Indonesian and Australian officials on matters of mutual interest, " it said.

"The Indonesian government... stands ready to work with the Australian Government... to ensure the interests of both our people are fulfilled."

Tony Abbott says friction over boats is 'passing irritant'

Earlier today, Prime Minister Tony Abbott described tensions between the two countries over the Coalition's border protection policy as a "passing irritant".

"The last thing I would ever want to do is anything that doesn't show the fullest possible respect for Indonesia's sovereignty," he said.

"We are already at this very moment cooperating closely with the Indonesians... I don't believe that the incoming government will do anything that will put that cooperation at risk. We want to build on that."